Effect of the most significantly associated markers on the EBV for pCE in the Fleckvieh breed. The boxplots show the effects of the most significantly associated SNPs (A) and haplotypes (B) on chromosomes 14 and 21 separately and combined. The solid line represents the population mean, and the dotted lines indicate one standard deviation of the EBV.

Detailed view of the region on chromosome 14 delineated by the haplotype associated with the EBV for pCE. (A) Map of genes contained in this region. Red symbols indicate genes resequenced in this study. (B) P-values of 27 SNPs from analysis of association with the pCE EBV. The open black dots indicate results from genotyping of the entire study population, and the blue triangles represent P-values resulting from imputation based on 810 genotyped animals. (C) Heatmap of the pairwise linkage disequilibrium (r2). The triangle delineates a linkage disequilibrium block containing the most significantly associated SNPs, including the potentially functional ss250608721 variant in RPS20.

Eleven SNPs meet the genome-wide significance level of P < 1.14 × 10−6. SNPs are arranged in the order of increasing P-values for the association with the paternal calving ease EBV. The P-value for each trait x genotype combination is obtained by a principal components analysis - based approach to account for population stratification. The allelic substitution effect (α) is given for the minor allele in additive genetic standard deviations of the EBV. Physical positions are based on the UMD3.1 assembly of the bovine genome sequence.

TABLE 2

SNPs within the haplotype associated with the estimated breeding value (EBV) for paternal calving ease (pCE) on bovine chromosome 14

SNP

Physical position (bp)

Haplotype allele

Minor allele (allele frequency)

Eigenstrat statistic

P value

α

BTB-01953819

23,817,572

A

G (0.26)

0.37

0.54

0.03

Hapmap45796-BTA-25271

23,853,811

T

A (0.07)

5.39

0.02

−0.18

ss250608741*

23,884,989

G

A (0.09)

1.06

0.3

0.06

ARS-BFGL-BAC-8052

23,893,220

G

A (0.01)

6.72

9.55 × 10−3

−0.45

ARS-BFGL-NGS-97821

23,946,436

G

A (0.1)

0.98

0.32

0.07

ARS-BFGL-NGS-104268

24,057,354

A

A (0.12)

61.00

5.71 × 10−15

−0.58

BTA-91250-no-rs

24,145,838

A

A (0.1)

59.32

1.34 × 10−14

−0.62

BTB-01417924

24,182,406

G

G (0.13)

43.54

4.15 × 10−11

−0.46

ARS-BFGL-NGS-110427

24,326,513

A

G (0.11)

0.02

0.89

−0.01

Hapmap59686-rs29020689

24,365,162

A

A (0.14)

36.94

1.22 × 10−9

−0.40

ARS-BFGL-NGS-102351

24,407,125

G

G (0.25)

18.34

1.85 × 10−5

−0.21

BTB-01532239

24,437,778

A

A (0.28)

28.04

1.19 × 10−7

−0.26

BTB-01530788

24,524,205

A

G (0.34)

8.65

3.27 × 10−3

0.12

BTB-01530836

24,573,257

G

A (0.35)

4.30

0.04

0.07

BTB-00557585

24,607,527

A

G (0.35)

4.75

0.04

0.08

BTB-00557532

24,643,266

A

G (0.35)

4.53

0.03

0.07

ss250608762*

24,759,177

G

T (0.01)

1.00

0.32

−0.14

Hapmap40120-BTA-34288

24,787,245

C

A (0.09)

0.28

0.6

−0.05

ss250608721*

24,954,981

A

A (0.16)

58.57

1.96 × 10−14

−0.47

ss250608720*

24,955,318

T

C (0.32)

3.56

0.06

0.06

Hapmap41234-BTA-34285

25,107,556

G

A (0.04)

13.89

1.94 × 10−4

−0.42

BTB-02056709

25,175,950

A

G (0.18)

2.55

0.11

−0.08

BTB-00559128

25,215,027

A

G (0.21)

0.01

0.92

0.00

BTB-00557354

25,254,540

G

A (0.12)

1.63

0.2

0.09

Hapmap46986-BTA-34282

25,307,116

A

G (0.46)

9.62

1.93 × 10−3

0.13

BTB-01779799

25,351,733

G

A (0.44)

19.00

1.30 × 10−5

0.19

Hapmap46735-BTA-86653

25,401,722

G

G (0.2)

34.40

4.48 × 10−9

−0.36

Twenty-three SNPs belong to the BovineSNP50 Bead chip collection and four additional SNPs designated by * result from resequencing. The P-values were obtained by using a principal components analysis-based approach to account for population stratification. Genotypes for SNPs resulting from resequencing were determined in 810 animals and imputed for the remaining 990 animals of the study population. The allelic substitution effect (α) is given for the minor allele in additive genetic standard deviations of the pCE EBV. SNPs are arranged according to their physical position, on the basis of UMD3.1 assembly of the bovine genome sequence.

The Genetics Society of America (GSA), founded in 1931, is the professional membership organization for scientific researchers and educators in the field of genetics. Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level.